Indo-Malay Archipelago Research Articles

Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli

The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.

The Indo-Pacific Stingray Genus Brevitrygon (Myliobatiformes: Dasyatidae): Clarification of Historical Names and Description of a New Species, B. manjajiae sp. nov., from the Western Indian Ocean

Members of the genus Brevitrygon are small, locally abundant tropical stingrays (family Dasyatidae) occurring in soft sedimentary habitats of inner continental shelves of the Indo-West Pacific from the Red Sea to Indonesia. Formerly members of the genus Himantura, whose members lack dorsal and ventral skin folds on the tail (typical of most dasyatid genera), folds are present or rudimentary in some Brevitrygon. Important to artisanal fisheries and known to consist of at least five species, these fishes are possibly the most frequently misidentified of all stingrays. Most were inadequately described in the 19th century, and they are often taxonomically confused due to morphological similarity, ontogenetic variability, and sexual dimorphism. Their nomenclatural history is complex with four of the known species represented within the type series of one species, B. walga (Müller & Henle). Also, the type of the species with which B. walga is most often confused, B. imbricata (Bloch & Schneider) from off southern India and Sri Lanka, is in very poor condition. A lectotype has been designated for B. walga (confined to the Bay of Bengal). The genus also contains B. heterura (Bleeker) from the Indo-Malay Archipelago, B. javaensis (Last & White) from off southern Indonesia, and a new species, B. manjajiae sp. nov., from the western Indian Ocean. The former species are redescribed and redefined based largely on a combination of morphometrics, tail morphology, squamation, and molecular data. Molecular divergences were detected within lineages of B. heterura, B. walga and B. manjajiae sp. nov., requiring further investigation.

The genus Ophelina Örsted, 1843 (Annelida: Opheliidae) in the coast of Kuwait (northern Indian Ocean), with the description of a new species

Two species of the genus Ophelina Örsted, 1843 (Annelida, Opheliidae) are reported from the coast of Kuwait (Arabian Gulf) after specimens collected in the intertidal and shallow subtidal, namely Ophelina arabica sp. nov. and Ophelina grandis (Pillai, 1961). The new species is mainly characterised by features of the anal tube, which is provided with about 25 annulations at each side; the ventral margins are fully fused while dorsal margins are fused at most of their length but are free at the distal end in the shape of a conspicuous incision; the posterior end is opened with free margins; the anal tube also lacks marginal papillae but bears a pair of basal papillae and an unpaired anal cirrus attached to ventral margin at mid-length. Ophelina grandis is reported for the first time in the Arabian Gulf; specimens are fully described and compared with similar species. A key for species of Ophelina in the Indo-Pacific, Southern Asia, Indo-Malay Archipelago and Australia, is also provided.

Fruit Size in Indo-Malayan Island Plants Is More Strongly Influenced by Filtering than by In Situ Evolution.

AbstractCommunity trait assembly, the formation of distributions of phenotypic characteristics across coexisting species, can occur via two main processes: filtering of trait distributions from the regional pool and in situ phenotypic evolution in local communities. But the relative importance of these processes remains unclear, largely because of the difficulty in determining the timing of evolutionary trait changes and biogeographic dispersal events in phylogenies. We assessed evolutionary and biogeographic transitions in woody plant species across the Indo-Malay archipelago, a series of island groups where the same plant lineages interact with different seed disperser and seed predator assemblages. Fruit size in 2,650 taxa spanning the angiosperm tree of life tended to be smaller in the Sulawesi and Maluku island groups, where frugivores are less diverse and smaller bodied, than in the regional source pool. While numerous plant lineages (not just small-fruited ones) reached the isolated islands, colonists tended to be the smaller-fruited members of each clade. Nearly all of the evolutionary transitions to smaller fruit size predated, often substantially, organismal dispersal to the islands. Our results suggest that filtering rather than within-island evolution largely determined the distribution of fruit sizes in these regions.

Phylogeography of Long-spined Sea Urchin Diadema setosum Across the Indo-Malay Archipelago.

Widely distributed, broadcast-spawning Diadema sea urchins have been used as model invertebrate species for studying the zoogeography of the tropical Indo-Pacific. So far, the Indo-Malay archipelago, a wide and geographically complex maritime region extending from the eastern Indian Ocean to the western Pacific Ocean, has been under-sampled. This study aims to fill this sampling gap and uncover the phylogeographic structure of the long-spined sea-urchin D. setosum in the central Indo-West pacific region. D. setosum samples (total N = 718) were collected in 13 sites throughout the Indo-Malay archipelago. We sequenced over 1157 bp of COI gene. The Phylogeographic structure was derived from pairwise ФST estimates using multidimensional scaling and hierarchical clustering analysis; biogeographic hypotheses were tested by AMOVA; genetic relationships between haplotypes were summarised in the form of a minimum-spanning network; and pairwise mismatch distributions were compared to the expectations from demographic and spatial expansion models. All samples from the Indo-West Pacific were of the previously uncovered D. setosum-a lineage. Phylogeographic structure was evident: the Andaman Sea population and the northern New Guinea population were genetically distinct. Subtler but significant haplotype-frequency differences distinguished two populations within the Indonesian seas, distributed in a parapatric-like fashion. The phylogeographic partition observed was insufficiently explained by previous biogeographic hypotheses. The haplotype network showed a series of closely related star-shaped haplogroups with a high proportion of singletons. Nucleotide-pairwise mismatch patterns in the two populations from the Indonesian seas were consistent with both demographic and spatial expansion models. While geographic barriers to gene flow were inferred at the western and eastern extremities of the Indo-Malay archipelago, the subtler parapatric pattern observed within the Indonesian seas indicated restriction in gene flow, in a fashion that can hardly be explained by geographic isolation given the dynamic current systems that cross this region. Our results thus raise the hypothesis of subtle reproductive isolation between ecologically incompatible populations. While the coalescence pattern of the Andaman-Sea population suggested demographic stability over evolutionary timescales, that of the two populations from the Indonesian seas indicated recent population expansion, possibly linked to the rapid changes in available D. setosum habitat caused by sea-level oscillations in the late Pleistocene. The phylogeographic patterns observed in this study point to likely allopatric differentiation in the central Indo-West Pacific region. Genetic differences between populations were likely reinforced during interglacials by some form of reproductive isolation.

The Influence of Muhammad Abduh in The Nusantara: From Qur’anic Exegesis to Islamic Reform Movement

This paper aims to present a survey of Abduh's extensive influence on Islamic reform (tajdid) in the Indo-Malay Archipelago, which often called Nusantara. Muhammad Abduh had a remarkable and lasting impact on religious thought and movement in Nusantara. His works and ideas were influential in the political and social landscape. He strongly impacted the movements of Muhammadiyah, al-Irsyad, Persatuan Islam (Persis), and Sarekat Islam. His Tafsir al-Manar brought inspiration with a rational outlook that influenced major tafsir works such as Tafsir al-Azhar, Tafsir al-Quranul Karim, Tafsir al-Qur'an al-Madjied (Tafsir al-Nur), Tafsir al-Qur'an al-Hakim, Tafsir al-Misbah, and Tafsir al-Furqan. The al-Manar magazine initiated by Muhammad Abduh significantly inspired many reform-oriented works and periodicals such as journal al-Imam, al-Munir, al-Ikhwan, Saudara, al-Dhakhirah al-Islamiyah, Qalam, and Seruan Azhar.

Can sea snakes slither through seascape structure? Comparative phylogeography and population genetics of Hydrophis group sea snakes in Australia and Southeast Asia

Pleistocene sea level changes substantially shaped the biogeography of northern Australia and the Indo-Malayan Archipelago (IMA). For co-distributed species, their phylogeographic and population genetic patterns are expected to be concomitant with geological transformations of the Pleistocene. However, species-specific ecologies and life history traits may also be influential in generating patterns which depart from simple expectations arising from biogeographic features. Thus, comparative population genetic studies, which use taxa that reduces variation in taxonomy and geography, may refine our understanding of how biogeographic elements shape the populations of co-occurring species. Here, we sampled two sea snake species, Hydrophis curtus and H. elegans, throughout their known ranges in the IMA and northern Australia. These sea snakes have similar life history strategies and ecologies as well as overlapping distributions across the Torres Strait, a well-known biogeographic feature. We analysed two mitochondrial DNA (mtDNA) fragments and 10 microsatellite loci using traditional population genetic approaches and used Bayesian clustering methods to examine species- specific phylogenetic relationships, genetic diversities, and population genetic structures. For both species, we found a consistent lack of significant genetic variation among sampling sites across the Gulf of Carpentaria (GOC) and the Great Barrier Reef (GBR). Similarly, Bayesian clustering showed no to weak genetic partitioning across the historical Torres Strait land bridge. Both species sampled in Australia displayed population expansion signatures in tests using mtDNA and microsatellite markers. We conclude that the phylogeographic and population genetic patterns of these sea snake species do not align with the Torres Strait land bridge. This lack of population genetic structure departs from previous findings on Aipysurus sea snakes and may be linked to the association of Hydrophis species to soft sediment habitats typically found across northern Australia. These divergent patterns between the sea snake groups present the importance of considering taxon-specific attributes in formulating conservation strategies.

Strong genetic structure and limited connectivity among populations of Clark’s Anemonefish (Amphiprion clarkii) in the centre of marine biodiversity

Populations of anemonefish species often show signs of local isolation due to limited dispersal potential and oceanographic conditions. Additionally, anthropogenic pressure, such as overharvesting and coral reef exploitation causes reduced population size, eventually leading to local extinction. The understanding of the genetic population structure, as well as the influence of both historical and current connectivity, is required to design effective marine protected area (MPA) networks. In this study, the genetic structure of Clark’s Anemonefish (Amphiprion clarkii) based on 209 individuals from 16 samples sites in the Indo-Malay Archipelago (IMA) is assessed through mitochondrial control region (mtCR) sequences and eight nuclear microsatellite loci. Results provided evidence of a significant genetic structure (mtCR: Φst = 0.42, Φct = 0.64; microsatellites: Fst = 0.01, Fct = 0.05). Genetic breaks were identified among Western (Padang Karimunjawa), Central (Sulawesi, Borneo, Bali, Komodo, Timor) and Eastern (Biak) IMA populations, with almost no gene flow. This matches with patterns obtained for congeneric and other coral reef taxa. Due to the restricted connectivity among these three regions, it is suggested to consider them as separate management areas in the design of MPA networks.

Phylogeography of Blue Corals (Genus Heliopora) Across the Indo-West Pacific

Species delimitation of corals is one of the most challenging issues in coral reef ecology and conservation. Morphology can obscure evolutionary relationships, and molecular datasets are consistently revealing greater within-species diversity than currently understood. Most phylogenetic studies, however, have examined narrow geographic areas and phylogeographic expansion is required to obtain more robust interpretations of within- and among- species relationships. In the case of the blue coral Heliopora, there are currently two valid species (H. coerulea and H. hiberniana) as evidenced by integrated genetic and morphological analyses in northwestern Australia. There are also two distinct genetic lineages of H. coerulea in the Kuroshio Current region that are morphologically and reproductively different from each other. Sampling from all Heliopora spp. across the Indo-Pacific is essential to obtain a more complete picture of phylogeographic patterns. To examine phylogenetic relationships within the genus Heliopora, we applied Multiplexed inter simple sequence repeat (ISSR) Genotyping by sequencing (MIG-seq) on > 1287 colonies across the Indo-West Pacific. Maximum likelihood phylogenetic trees indicated the examined Heliopora samples comprise three genetically distinct groups: H. coerulea group, H. hiberniana group, and a new undescribed Heliopora sp. group with further subdivisions within each group. Geographic structuring is evident among the three species with H. hiberniana group found in the Indo-Malay Archipelago and biased toward the Indian Ocean whilst Heliopora sp. was only found in the Kuroshio Current region and Singapore, indicating that this taxon is distributed in the western Pacific and the Indo-Malay Archipelago. Heliopora coerulea has a wider distribution, being across the Indian Ocean and western Pacific. This study highlights the effectiveness of phylogenetic analysis using genome-wide markers and the importance of examining populations across their distribution range to understand localized genetic structure and speciation patterns of corals.

Mitochondrial Markers Identify a Genetic Boundary of the Green Tiger Prawn (Penaeus semisulcatus) in the Indo-Pacific Ocean.

A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region.

A review of the genus Rusa in the indo-malayan archipelago and conservation efforts.

Genus Rusa, belonging to the deer family Cervidae is native to the Indo-Malaya Archipelago (IMA). However, detailed information on the Rusa genus in the IMA is limited. This review provides comprehensive information on the Rusa genus in the IMA including, threats and conservation efforts. There are four species of deer in Rusa genus, which is Sambar deer (Rusa unicolor), Javan deer (Rusa timorensis), Visayan spotted deer (Rusa alfredi) and Philippine deer (Rusa marianna). Despite their wide distribution in the South Asian and Southeast Asian regions, they are under serious threats. Some conservation efforts that are being done to protect and conserve them among others are; (1) facilities protection, (2) habitat enrichment programme, (3) Ex-situ conservation, (4) legislations, and (5) captive breeding. Conservation through genetics is also an important step in conserving these species. Recommendations for conservation of the genus are also discussed; 1. maintenance of ecosystem. 2. more effective monitoring system on the existing protected area. 3. ex-situ conservation, and 4. habitat monitoring.

Comparative genetic stock structure in three species of commercially exploited Indo‐Malay Carangidae (Teleosteii, Perciformes)

We examine genetic structuring in three commercially important species of the teleost family Carangidae from Malaysian waters: yellowtail scad Atule mate, bigeye scad Selar crumenophthalmus and yellowstripe scad Selaroides leptolepis, from the Indo-Malay Archipelago. In view of their distribution across contrasting habitats, we tested the hypothesis that pelagic species display less genetic divergence compared with demersal species, due to their potential to undertake long-distance migrations in oceanic waters. To evaluate population genetic structure, we sequenced two mitochondrial (mt)DNA [650 bp of cytochrome oxidase I (coI), 450 bp of control region (CR)] and one nuclear gene (910 bp of rag1) in each species. One hundred and eighty samples from four geographical regions within the Indo-Malay Archipelago including a population of yellowtail from Kuwait were examined. Findings revealed that the extent of genetic structuring among populations in the semi-pelagic and pelagic, yellowtail and bigeye were lower than demersal yellowstripe, consistent with the hypothesis that pelagic species display less genetic divergence compared with demersal species. The yellowtail phylogeny identified three distinct clades with bootstrap values of 86%-99% in mtDNA and 63%-67% in rag1. However, in bigeye, three clades were also observed from mtDNA data while only one clade was identified in rag1 dataset. In yellowstripe, the mtDNA tree was split into three closely related clades and two clades in rag1 tree with bootstraps value of 73%-99% and 56% respectively. However, no geographic structure appears in both mtDNA and rag1 datasets. Hierarchical molecular variance analysis (AMOVA), pair wise FST comparisons and the nearest-neighbour statistic (Snn ) showed significant genetic differences among Kuwait and Indo-Malay yellowtail. Within the Indo-Malay Archipelago itself, two distinct mitochondrial lineages were detected in yellowtail suggesting potential cryptic species. Findings suggests varying degrees of genetic structuring, key information relevant to management of exploited stocks, though more rapidly evolving genetic markers should be used in future to better delimit the nature and dynamics of putative stock boundaries.

Concise review of the genus Caulerpa J.V. Lamouroux

The genus Caulerpa is highly diverse, especially in the Caribbean Sea, the Indo-Malay archipelago and the temperate waters of southern Australia. Currently, more than 100 species are recognized worldwide. Despite recent advances in taxonomy and phylogeny, there is still confusion about the delimitation and identification of some species due to tremendous phenotypic plasticity. Caulerpa is known to occupy a wide range of environmental niches and to have great invasive potential. More studies are necessary to understand better the ecology (invasiveness, the functional role of its microbiome) and the biology (reproduction, life cycle, and metabolism) of Caulerpa species, especially for economical species. Very few species, mainly C. lentillifera and C. racemosa known as green caviar, have been cultivated. Caulerpa is consumed mostly in Asia and Oceania, but its popularity tends to be on the increase in western countries with new nutritional practices (vegetarians, vegans, health foods). Being naturally enriched in essential nutrients and various health-promoting compounds, Caulerpa species are promising candidates for the design of functional foods and in the health and well-being sectors. The diversity of Caulerpa offers a remarkable potential for valorization with innovation opportunities. Caulerpa farming can bring significant economic and environmental (e.g., bioremediation, blue carbon pump) benefits if these farms are established in a sustainable approach.

The pattern of HLA-A, -B and -DRB1 alleles and haplotypes of four Malay sub-ethnic groups namely Kelantan, Champa, Patani and Mandailing Malays of Peninsular Malaysia

“Bumiputra” or “son of the soil” is a term used to represent the Malays and other indigenous populations of Malaysia. The Malays are Austronesian speaking population and originated from different parts of the Indo-Malay Archipelago. The migration of Malay population from different parts of Indo-Malay Archipelago were mainly due to trading purposes which shaped the current Malay sub-ethnic groups with unique culture and with distinctive dialects. In this study, HLA typing was carried out using Sequence-based Typing (SBT) method on 109 individuals comprising of four Malay sub-ethnic groups namely Kelantan (n = 28), Champa (n = 29), Patani (n = 25) and Mandailing (n = 27) Malays. The HLA data is available in the Allele Frequencies Net Database (AFND).

Patterns and drivers of species diversity in the Indo‐Pacific red seaweed Portieria

AbstractAimBiogeographical processes underlying Indo‐Pacific biodiversity patterns have been relatively well studied in marine shallow water invertebrates and fishes, but have been explored much less extensively in seaweeds, despite these organisms often displaying markedly different patterns. Using the marine red alga Portieria as a model, we aim to gain understanding of the evolutionary processes generating seaweed biogeographical patterns. Our results will be evaluated and compared with known patterns and processes in animals.LocationIndo‐Pacific marine region.MethodsSpecies diversity estimates were inferred using DNA‐based species delimitation methods. Historical biogeographical patterns were inferred based on a six‐gene time‐calibrated phylogeny, distribution data of 802 specimens, and probabilistic modelling of geographical range evolution. The importance of geographical isolation for speciation was further evaluated by population genetic analyses at the intraspecific level.ResultsWe delimited 92 candidate species, most with restricted distributions, suggesting low dispersal capacity. Highest species diversity was found in the Indo‐Malay Archipelago (IMA). Our phylogeny indicates that Portieria originated during the late Cretaceous in the area that is now the Central Indo‐Pacific. The biogeographical history of Portieria includes repeated dispersal events to peripheral regions, followed by long‐term persistence and diversification of lineages within those regions, and limited dispersal back to the IMA.Main conclusionsOur results suggest that the long geological history of the IMA played an important role in shaping Portieria diversity. High species richness in the IMA resulted from a combination of speciation at small spatial scales, possibly as a result of increased regional habitat diversity from the Eocene onwards, and species accumulation via dispersal and/or island integration through tectonic movement. Our results are consistent with the biodiversity feedback model, in which biodiversity hotspots act as both “centres of origin” and “centres of accumulation,” and corroborate previous findings for invertebrates and fish that there is no single unifying model explaining the biological diversity within the IMA.

Strong genetic differentiation in tropical seagrass Enhalus acoroides (Hydrocharitaceae) at the Indo-Malay Archipelago revealed by microsatellite DNA.

The Indo-Malay Archipelago is regarded as a barrier that separates organisms of the Indian and Pacific Oceans. Previous studies of marine biota from this region have found a variety of biogeographic barriers, seemingly dependent on taxon and methodology. Several hypotheses, such as emergence of the Sunda Shelf and recent physical oceanography, have been proposed to account for the genetic structuring of marine organisms in this region. Here, we used six microsatellite loci to infer genetic diversity, population differentiation and phylogeographic patterns of Enhalus acoroides across the Indo-Malay Archipelago. Heterozygosities were consistently high, and significant isolation-by-distance, consistent with restricted gene flow, was observed. Both a neighbour joining tree based on DA distance and Bayesian clustering revealed three major clusters of E. acoroides. Our results indicate that phylogeographic patterns of E. acoroides have possibly been influenced by glaciation and deglaciation during the Pleistocene. Recent physical oceanography such as the South Java Current and the Seasonally Reversing Current may also play a role in shaping the genetic patterns of E. acoroides.

Evolutionary cascades induced by large frugivores

Large, fruit-eating vertebrates have been lost from many of the world's ecosystems. The ecological consequences of this defaunation can be severe, but the evolutionary consequences are nearly unknown because it remains unclear whether frugivores exert strong selection on fruit traits. I assessed the macroevolution of fruit traits in response to variation in the diversity and size of seed-dispersing vertebrates. Across the Indo-Malay Archipelago, many of the same plant lineages have been exposed to very different assemblages of seed-dispersing vertebrates. Phylogenetic analysis of >400 plant species in 41 genera and five families revealed that average fruit size tracks the taxonomic and functional diversity of frugivorous birds and mammals. Fruit size was 40.2-46.5% smaller in the Moluccas and Sulawesi (respectively), with relatively depauperate assemblages of mostly small-bodied animals, than in the Sunda Region (Borneo, Sumatra, and Peninsular Malaysia), with a highly diverse suite of large and small animals. Fruit color, however, was unrelated to vertebrate diversity or to the representation of birds versus mammals in the frugivore assemblage. Overhunting of large animals, nearly ubiquitous in tropical forests, could strongly alter selection pressures on plants, resulting in widespread, although trait-specific, morphologic changes.

Mitochondrial DNA analyses of narrow-barred Spanish mackerel (Scomberomorus commerson) sampled from the Arabian Sea, the Bay of Bengal, and the Indo-Malay archipelago

The phylogeography of the narrow-barred Spanish mackerel (Scomberomorus commerson) in the Arabian Sea, Bay of Bengal, Indian Ocean, Java Sea, and South China Sea was investigated using sequence dat...

Phylogeography of Noah’s giant clam

Noah’s giant clam (Tridacna noae), recently resurrected from synonymy with T. maxima, occurs from Christmas Island to the Northern Line Islands and from the Ryukyu Islands to New Caledonia. We used mitochondrial and microsatellite markers to investigate the phylogeographic structure and demographic history of T. noae over most of its geographical range. Results from the two types of markers reveal a consistent population structure, partitioning T. noae into three distinct lineages: (1) eastern half of the Indo-Malay archipelago and Western Australia, (2) Melanesia and Micronesia, and (3) Central Polynesia. Demographic expansion initiated between 300,000 and 400,000 years ago, as was detected for each haplogroup. This pattern, which is congruent with other co-occurring Tridacna species, indicates a shared evolutionary history with expansion from past refuges following late-Pleistocene sea-level changes.

Concordance of microsatellite and mitochondrial DNA markers in detecting genetic population structure in the boring giant clam Tridacna crocea across the Indo‐Malay Archipelago

AbstractMitochondrial DNA (mtDNA) is a single, usually non‐recombining locus, and often uniparentally inherited. Therefore, its ability to reveal recent gene flow among populations is usually questioned. In this study, the genetic population structure of 16 populations of Tridacna crocea (n = 366) from the Indo‐Malay Archipelago (IMA) was examined with 10 microsatellite markers and compared to previous studies using mtDNA, in order to test if the revealed population structure was congruent between the two marker systems. The results showed that the genetic population structure revealed by the two marker systems was mostly congruent, with a high correlation between cytochrome c oxidase subunit I (COI) and microsatellites. The studied populations could be divided by both marker systems as follows: (i) Eastern Indian Ocean, (ii) Central IMA, and (iii) Western Pacific. Populations in the Central IMA showed high gene flow. However, populations in the Java Sea (Karimunjava, Pulau Seribu) were grouped into a separate cluster by mtDNA analysis, while this grouping was not detected by microsatellites. It was also noteworthy that there is obvious heterozygosity deficiency in most of the populations, which may be caused by null alleles, inbreeding or population expansion. Overall, these results indicate that the mitochondrial COI gene is applicable for population genetic analysis and precise recovery of connectivity patterns of giant clams. Therefore, the combination of mtDNA and nuclear DNA markers can lead to a more complete understanding of population genetics. Moreover, this study is expected to facilitate fully displaying the population genetic structure of giant clams combining with other researchers' results.